Exploration of cultivable fungal communities in deep coal‐bearing sediments from ∼1.3 to 2.5 km below the ocean floor

Abstract

Although subseafloor sediments are known to harbour a vast number of microbial cells, the distribution, diversity, and origins of fungal populations remain largely unexplored. In this study, we cultivated fungi from 34 of 47 deep coal-associated sediment samples collected at depths ranging from 1289 to 2457 m below the seafloor (mbsf) off the Shimokita Peninsula, Japan (1118 m water depth). We obtained a total of 69 fungal isolates under strict contamination controls, representing 61 Ascomycota (14 genera, 23 species) and 8 Basidiomycota (4 genera, 4 species). Penicillium and Aspergillus relatives were the most dominant genera within the Ascomycetes, followed by the members of genera Cladosporium, Hamigera, Chaetomium, Eutypella, Acremonium, Aureobasidium, Candida, Eurotium, Exophiala, Nigrospora, Bionectria and Pseudocercosporella. Four Basidiomycota species were identified as genera Schizophyllum, Irpex, Bjerkandera and Termitomyces. Among these isolates, Cladosporium sphaerospermum and Aspergillus sydowii relatives were isolated from a thin lignite coal-sandstone formation at 2457 mbsf. Our results indicate that these cultivable fungal populations are indigenous, originating from past terrigenous environments, which have persisted, possibly as spores, through ∼20 million years of depositional history.

Evaluation of reported sediment samples from 20 Ma using a molecular phylogenetic approach: comment on Liu et al. (2017)

“…White boxes represent modern samples and black boxes represent ancient samples sequenced by Liu et al . (). In Case 1, molecular evolution of the fungal populations buried in deep subseafloor sediments has occurred continuously over the past 20 million years.…”

“…Liu et al . () used samples from 1.3 to 2.5 km below the ocean floor. If the fungal DNA sequences they reported were not contaminated, two interpretations are possible (Fig.…”

“…Because the studies by Liu et al . () and Imachi et al . () would overturn the conventional wisdom on ancient DNA longevity, it is again essential to carefully evaluate the authenticity of their sample dating.…”

“…Here, we used the phylogenetic approach to evaluate the 20‐Ma age of the DNA sequences from fungal isolates reported by Liu et al . ().…”

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“…Over the course of nearly 50 years of scientific ocean drilling, microbial cells have been found everywhere, even in sediments of Cretaceous age (Roussel et al, 2008), in extremely nutrient poor sediment below the ocean gyres (D'Hondt et al, 2009(D'Hondt et al, , 2015, in the deepest sampled coal-bearing sediments (~2500 meters below seafloor [mbsf ]) Glombitza et al, 2016;Liu et al, 2017), and in basement rocks (Orcutt et al, 2011;Lever et al, 2013). Metabolic rates of deep subseafloor microbes are extraordinarily low (D'Hondt et al, 2002(D'Hondt et al, , 2004, with most deeply buried microbial cells physiologically active Imachi et al, 2011;Inagaki et al, 2015) or quiescent as dormant phase or spore Langerhuus et al, 2012).…”